Over a million patients with HIV/AIDS are currently afflicted with fungal meningoencephalitis, and the resultant morbidity and mortality are profoundly significant. The vast majority of these infections are caused by strains of Cryptococcus neoformans var. grubii, which have been recognized by possessing capsular serotype A. This yeast is ubiquitous in the environment, where it is associated with avian habitats and vegetative debris. Infection is not contagious but acquired exogenously by the inhalation of desiccated yeast cells or basidiospores. Although the ability to infect mammals offers no obvious evolutionary advantage to the fungus, most natural isolates are capable of colonizing mammalian hosts, which suggests that pathogenicity evolved in the environment. In preliminary studies, we developed robust multilocus genotyping methods and discovered two unique, genetically isolated subpopulations of serotype A: (i) a global subpopulation comprised of ubiquitous, highly clonal monomorphic strains associated with the excreta of feral pigeons and (ii) a unique, highly-variable, recombining subpopulation in southern Africa that is associated with indigenous African trees. The genetic diversity of this southern African population is unprecedented and suggests that this population may represent ancestral origin of the extant, global strains of serotype A. We also analyzed the frequencies of multilocus genotypes among clinical and environmental samples and discovered that not all strains (or genotypes) are equally likely to cause cryptococcal disease in humans. Despite the enormous diversity of genotypes in the African population, almost half of all patients in Botswana (46%) and a major proportion of patients in South Africa (17%) were infected by strains with three closely related genotypes. In contrast, the distribution of genotypes among environmental isolates in Africa is comparable, and none are dominant. Among global isolates, most genotypes were equally prevalent in both patients and the predominant non-African ecological niche, pigeon feces, although one genotype (A2) was highly prevalent in the environment but never isolated from patients. This proposal will investigate the evolution of pathogenicity in C. neoformans at the population genetic and genomic levels. This project involves two independent but complementary aims. Aim 1 will use methods of population genetic and phylogenetic analysis to test the hypothesis of the African origin of serotype A. Aim 2 will use methods of comparative genomics, genome-wide association mapping and phenotypic assays to identify genomic regions that differentiate strains that frequently cause infection from strains that are rarely, if ever, isolated from humans. This application of whole-genome methods to natural strains of C. neoformans will identify genes or genomic regions that are significantly associated with pathogenicity for humans. PUBLIC HEALTH RELEVANCE: This project will utilize methods of population genetics, comparative genomics and the whole-genome association mapping to study evolution of pathogenesis of Cryptococcus neoformans, a leading cause of fungal meningoencephalitis. The project provides a paradigm for studying the population genetics and evolution of other opportunistic and emerging pathogens.